Parsimonious Kernel Fisher Discrimination

By applying recent results in optimization transfer, a new algorithm for kernel Fisher Discriminant Analysis is provided that makes use of a non-smooth penalty on the coefficients to provide a parsimonious solution. The algorithm is simple, easily programmed and is shown to perform as well as or better than a number of leading machine learning algorithms on a substantial benchmark. It is then applied to a set of extreme small-sample-size problems in virtual screening where it is found to be less accurate than a currently leading approach but is still comparable in a number of cases

A Simple Iterative Algorithm for Parsimonious Binary Kernel Fisher Discrimination

By applying recent results in optimization theory variously known as optimization transfer or majorize/minimize algorithms, an algorithm for binary, kernel, Fisher discriminant analysis is introduced that makes use of a non-smooth penalty on the coefficients to provide a parsimonious solution. The problem is converted into a smooth optimization that can be solved iteratively with no greater overhead than iteratively re-weighted least-squares. The result is simple, easily programmed and is shown to perform, in terms of both accuracy and parsimony, as well as or better than a number of leading machine learning algorithms on two well-studied and substantial benchmarks

Contour prairie strips alter microbial communities and functioning both below and in adjacent cropland soils

Prairie strips are narrow strips of native, perennial vegetation (10–40 m width) integrated within cropped fields to provide benefits for water quality and biodiversity. However, the impact of prairie strips on soil microbial communities and function, both underneath the prairie strips and in the adjacent cropland, is not known. We assessed the effect of restoring native perennial vegetation on soil C and N, potential enzyme activities (PEA), and microbial community composition in the soil directly underneath and cropland adjacent (0.1 to 9 m) to 12-year-old prairie strips integrated within row crop fields. We found that prairie strips consistently increased soil microbial biomass carbon (>56 %) and altered PEA in complex ways. Generally, prairie strips increased hydrolase and decreased oxidoreductase PEA. Prairie strips also changed the soil microbial community directly under prairie vegetation, and, contrary to the expectation that greater plant diversity leads to greater soil microbial diversity, prairie strips reduced bacterial and fungal diversity. The prairie strip's effect on adjacent cropland soils depended on year, but it was strong when it occurred and was typically independent of distance from the prairie strip. Prairie strips increased PEA in adjacent soils (<9 m) by as much as 38 % and shifted bacterial and fungal beta diversity, but neither showed patterns with distance from the prairie strip, indicating that prairie strips cause field-scale shifts in soil biota and functioning, and these effects are not mediated by proximity to the prairie strip. Understanding the mechanisms underlying prairie strips' impact on soil biota, both underneath and adjacent to the prairie, is key to optimize their agroecosystem benefits.This article is published as Dutter, Cole R., Corinn E. Rutkoski, Sarah E. Evans, and Marshall D. McDaniel. "Contour prairie strips alter microbial communities and functioning both below and in adjacent cropland soils." Applied Soil Ecology 199 (2024): 105424. doi:10.1016/j.apsoil.2024.105424. © 2024 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Cover crops have positive and negative effects on soil properties and crop yield over a 15-year timespan

Winter cover crops (WCC) have received much attention due to their environmental benefits, particularly improvements to soil health. However, most studies are made less than 5 years after implementation, and there is no consensus about when to soil sample to best quantify a WCC effect. We used a paired, chronosequence approach with 1–15 years since implementation of cereal rye (Secale cereale) as a WCC, and analyzed soils collected in spring and autumn. We measured soil bulk density, maximum water-holding capacity, penetration resistance, pH, total carbon (C) and nitrogen (N), permanganate oxidizable carbon, microbial biomass carbon (MBC), and microbial biomass N, potentially mineralizable carbon (PMC), and potentially mineralizable nitrogen (PMN). We also analyzed maize (Zea mays) and soybean (Glycine max) grain yield. We found that WCC increased MBC and PMC by 8% each and increased PMN by 11%, regardless of time-since-implementation. Furthermore, sampling biological soil health indicators in the spring resulted in more positive, significant treatment effects (12%–19%) compared to sampling in the autumn, where we found no effect. WCC increased soybean yields by 7% after 8–9 years but decreased maize yield by 23% after 15 years. WCC reduced soil penetration resistance by 10% after 8–9 years but increased it by 20% after 15 years. These later contrasting results may be due to management nuances or biophysical changes in cropping systems with time. Overall, WCC have many environmental benefits, and in our study, WCC increase biological soil health indicators quickly, but yield drag and increased soil penetration resistance may occur later in WCC adoption.This article is published as Dutter, Cole R., Marshall D. McDaniel, Morgan P. Davis, Teresa A. Middleton, Stefan Gailans, and Sarah Carlson. "Cover crops have positive and negative effects on soil properties and crop yield over a 15‐year timespan." Soil Science Society of America Journal 89, no. 2 (2025): e70032. doi:10.1002/saj2.70032.Iowa Nutrient Research Center, College of Agriculture and Life Sciences, Iowa State University, Grant/Award Number: Grant #: E2017-10. Open access funding provided by the Iowa State University Library

Activation of heme biosynthesis by a small molecule that is toxic to fermenting Staphylococcus aureus

Staphylococcus aureus is a significant infectious threat to global public health. Acquisition or synthesis of heme is required for S. aureus to capture energy through respiration, but an excess of this critical cofactor is toxic to bacteria. S. aureus employs the heme sensor system (HssRS) to overcome heme toxicity; however, the mechanism of heme sensing is not defined. Here, we describe the identification of a small molecule activator of HssRS that induces endogenous heme biosynthesis by perturbing central metabolism. This molecule is toxic to fermenting S. aureus, including clinically relevant small colony variants. The utility of targeting fermenting bacteria is exemplified by the fact that this compound prevents the emergence of antibiotic resistance, enhances phagocyte killing, and reduces S. aureus pathogenesis. Not only is this small molecule a powerful tool for studying bacterial heme biosynthesis and central metabolism; it also establishes targeting of fermentation as a viable antibacterial strategy